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lecture exam 2 Flashcards

1
Q

electron acceptors in aerobic and anaerobic respiraton

A

aerobic: o2
anaerobic: NO3-, SO42-, CO2, Fe3+, SeO4

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2
Q

besides glycolysis, what are other ways to make 5C -> 6C

A
  1. Embden-Meyerhof
  2. **pentose phosphate/ hexomonophosphate
  3. Entner-Duodoroff
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3
Q

oxidative phosphorylation

A

ETC generates proton motor force –> ATP synthesis

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4
Q

Electron Transport Chain

A
  • building proton gradient outside cell
  • transfer from NADH + FADH2 –> terminal e- acceptor
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5
Q

what drives ATP conversion?

A

changing conformation of proteins using chemical gradient (ETC)

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6
Q

Fermentation

A
  • purpose: to remake oxidized form of NAD+ (NADH –> NAD+)
  • pyruvate used to reduce pH of environment
  • oxidative phosphorlyation doesn’t occur (ATP formed only by SLP)
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7
Q

standard reduction potential

A
  • gets more positive as e- use energy to move protons across membrane
  • more negative to more positive carriers
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8
Q

what bond connects phosphate group and sugar?

A

phosphodiester bond

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9
Q

what bond connects nucleotides?

A

hydrogen bond

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10
Q

what did Meselson-Stahl experiment show?

A

semi-conservative replication

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11
Q

how does DNA relieve stress on itself?

A

supercoiling- folds around on itself

structural uniqueness
* major groove 2.2 nm
* minor groove 1.2 nm

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12
Q

bacterial nucleoid

A

condensed DNA (30-50 loops of DNA) but 1 big circle

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13
Q

supercoiling stress

A
  • constraining supercoils
  • wrapping DNA around proteins
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14
Q

why does DNA have chemical polarity?

A
  • nucleotides are asymmetric
  • 5’ 3’
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15
Q

topoisomerase

A

modulates supercoiling of DNA
Topoisomerase 1
* cuts 1 strand and passes other strand through (changes DNA 1 supercoil at a time)
* relieves torsional stress caused by supercoils
Topoisomerase 2:
* cuts both strands and passes 2 other strands from somewhere else in DNA (change DNA 2 supercoils at a time)
* relieves negative supercoils (siproflaxin)
* ex: gyrase- adds negative supercoils (strands rotate and relive strain of unwinding

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16
Q

strand passage

A

topoisomerase binds to DNA –> breaks both strands –> passed DNA strands through break before resealing

enzyme holds the cut ends of DNA so don’t rotate

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17
Q

unsupercoiled DNA
and
positive vs negative supercoils

A

unsupercoiled: 1 wind for 10 bases
positive: overwinding
negative: underwinding (take more base pairs to get from one end to the other)

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18
Q

supercoils

A

twist and compact DNA

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19
Q

is bacterial DNA neg or pos supercoiled?

A

negative

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20
Q

archaeal topoisomerases

A

introduce positve supercoils

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21
Q

primosome

A

DnaA and DnaB bind to sequence at oriC and initiate replication

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22
Q

DNA helicase

A
  • Dna B
  • unwinds helix at replication fork (breaks HB)
  • melts DNA
  • recruits primase
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23
Q

primase

A
  • DnaG
  • lays down primers of RNA for DNA polymerase
  • forms 3’ OH for DNA to attach
  • recruits clamp loader
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24
Q

DNA polymerase III

A
  • does most of DNA replication 5’–>3’
  • needs primer bc cant prime itself
  • 3’ –> 5’ (exonucelase activity for proofreading)
  • 5’ –> 3’ (polymerase activity for DNA synthesis) (Nick translation activity)
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25
DNA polymerase I
proof reads fills in RNA primer gaps * 5'--> 3' (exonuclease activity for removal of RNA primer) * 3' --> 5' (exonucelase activity for proofreading) * 5' --> 3' (polymerase activity for DNA synthesis) (Nick translation activity)
26
RNase H
removes RNA primers
27
DNA ligase
* seals DNA by reforming phosphodiester bonds in backbone * links 3' OH with 5' phosphate groups
28
SSB
* single-strand DNA binding proteins * bind SSDNA @ replication fork and block rejoining * makes sure DNA is SS when polymerization machinery is ready to replicate it
29
replication fork
where 2 strands are separated and the new synthesis is occuring
30
difference between leading and lagging strand
leading: direction of fork along 5->3, polymerase stable on strand lagging: opposite direction of fork along 3->5, polymerase 3 released and reassembled
31
what structure coordinates activity between leading and lagging strand synthesis?
clamp loader
32
plasmids
extrachromosomal pieces of DNA
33
low-copy # plasmids
1 or 2 copies per cell ex: F plasmids (from conjugation)
34
high copy # plasmids
* up to 50 copies per cell * divide continuously * randomly segregate to daughter cells * if you have any large DNA fragments
35
thermocyclers
hot and cool tubes take pieces of DNA, identify polymerases, and replicate DNA
36
restriction enzymes
* cut DNA at specific sites * normally protect bacteria from viral DNA
37
RNA polymerase
binds DNA, reads sequence, polymerasizes RNA
38
sigma factor
* promoter * summons RNA polymerase to bind to target DNA sequence * 70: guides to most genes * 32: active when env problems * Bs32: active when stressed by heat
39
what do snRNA and miRNA do? | and type of snRNA
regulate transcription | mRNA: splicing in eukaryotes and archaea
40
Aminoacyl tRNA transferase
makes charged tRNA meth esterification
41
what is a ribosome made up of?
30s and 50s= 70s
42
what does 23s rRNA do?
moves P to A
43
are there more post transcription or translation modifications in bacteria?
post-translation
44
what enzymes modify translated proteins?
1. fMet (removed from N-term) 2. small groups added to a.a. (PO4, CH3, adenylate) 3. protesases (cleave/ degrade protein)
45
chaperone protein examples
GroEl-GroEs complex: chaperone protein that refolds denatured proteins w ATP (Hsp 60 and Hsp 10) barrel shape- protein to be refolded fits into center or binds to misfoled protein domains Dnak: Hsp 70 (heat shock) (cant do this on eukaryote cells because too big)
46
sec-dependent pathway
secretion pathway that delivers proteins to periplasm
47
signal sequence
* targets ribosome to plasma membrane * N-terminal amino acid * bound by signal recognition particle (SRP)
48
Type 1 secretion system
* secretes protein out of bacterium * type 4 (conjugation)
49
proteases
cut proteins at specific amino acid sequences
50
proteasomoes
degrade proteins (barrel shape)
51
inducer vs repressor molecules
inducer: innactivates repressor (cannot bind to DNA) (lac) corepressor: activates repressor (binds to DNA) (trp) | both change repressor conformation
52
what sugars make up lactose?
glucose and galactose
53
operon operator repressor
operon: cluster of genes operator: regulatory site rep: regulatory protein that blocks mRNA synthesis
54
trpR (repressor) mutants
* unliked: can be put anywhere in organism and will make repressor * recessive: can be fixed if you had another WT gene
55
trpOc (operator-constitutive) mutants
linked and dominant
56
what is cAMP
secondary messenger mediator of catabolite repression and E. coli
57
what is the activator for Lac transcription?
CAP
58
cya gene vs crp gene
cya: lacks adenylate cyclase (cell can't grow on fermentable carbon sources other than glucose unless medium has cAMP) crp: codes for cap
59
horizontal gene transfer
* movement of genes between cells (besides cell division) * transformation, conjugation, transduction
60
transposons vs plasmids
transposons: carry genes into chromosome plasmids: carry genes between cells without having to become part of chromosome
61
transition vs transversion point mutations
transition: pyrine -> purine transversion purine-> pyrimidine
62
silent vs missense mutation
silent: codes for same aa missense: changes codon
63
Ames test
* measurement of mutagens * uses strain auxotrophic for histidine * more colonies: stronger mutagen
64
transformation gene transfer
* DNA uptake from medium * competent cells take up exogenous DNA * translocasome takes up DNA
65
conjugation gene transfer
* move plasmid from one system to another * pilus protein (encoded on F factor) brings 2 cells together * in recipient cell, transfered DNA forms new F plasmid * Hfr: donor cell
66
transduction gene transfer
* virus transfers genetic material from one bacterium to another *
67
defense against transferred DNA
* add methyl groups to DNA bc cut unmeth * entering DNA destroyed by endonucleases (unless methylated or from similar species)

Microbio (5 decks)

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